Mitochondrial DNA from 400 thousand year old humans

The Sima de los Huesos (‘pit of bones’) site in the cave complex of Atapuerca in northern Spain has yielded one of the greatest assemblages of hominin bones. Well-preserved remains of at least 28 individuals date to the Middle Pleistocene (>300 ka). Anatomically the individuals have many Neanderthal-like features but also show affinities with earlier Homo heidelbergensis, who is widely considered to be the common ancestor for anatomically modern humans and Neanderthals, and perhaps also for the mysterious Denisovans. Most palaeoanthropologists have previously considered this Atapuerca group to be early Neanderthals, divergent from African lineages because they migrated to and became isolated in Europe.

English: Cranium 5 is one of the most importan...
Human cranium from the Sima de los Huesos, Atapuerca mountains (Spain). (credit: Wikipedia)

The riches of the Sima de los Huesos ossuary made it inevitable that attempts would be made to extract DNA that survived in the bones, especially as bear bones from the area had shown that mtDNA can survive more than 4300 ka. There has been an air of expectancy in hominin-evolution circles, and indeed among the wider public, since rumours emerged that the famous Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany had initiated genetic sequencing under the direction of Svante Pääbo: perhaps another ‘scoop’ to add to their reconstructing the first Neanderthal and Denisovan genomes. The news came out in the 5 December 2013 issue of Nature, albeit published on-line (Meyer, M. and 10 others 2013. A mitochondrial genome sequence of a hominin from Sima de los Huesos, Nature, v. 504; doi:10.1038/nature12788) with a discussion by Ewan Callaway (Callaway, E. 2013. Hominin DNA baffles experts Nature, v. 504, p. 16-17).

The bafflement is because the mtDNA from a femur of a 400 ka  individual does not match existing Neanderthal data as well as it does that of the Denisovan from Siberia by such a degree that the individual is an early Denisovan not a Neanderthal. Northern Spain being thousands of kilometres further west than the Denisova cave heightens the surprise.  Indeed, it may be on a lineage from an earlier hominin that did not give rise to Neanderthals. The full Neanderthal and Denisovan genomes suggest that they shared a common ancestor up to 700 ka ago. So the Sima de los Huesos individual presents several possibilities. It could be a member of an original population of migrants from Africa that occupied wide tracts of Eurasia, eventually to give rise to both Neanderthals and Denisovans. That genetic split may have arisen by the female line carrying it not surviving into populations that became Neanderthals – mtDNA is only present in the eggs of mothers. Mind you, that begs the question of who the Neanderthal females were. Another view is that the Sima de los Huesos individual may be descended from even earlier H. antecessor, whose 800 ka remains occur in a nearby cave. Pääbo’s team have even suggested that Denisovans interbred with a mysterious group: perhaps relics of the earlier H. antecessor colonists.

Established ideas of how humans emerged, based on bones alone and very few individuals to boot, are set to totter and collapse like a house of cards. Interbreeding has been cited three times from DNA data: modern human-Neanderthal; modern human-Denisovan and Denisovan with an unknown population. Will opinion converge on what seems to be obvious, that one repeatedly errant species, albeit with distinct variants, has been involved from far back in the human evolutionary journey?  There seems only one avenue to follow for an answer, which is to look for well preserved H. heidelbergensis. H. antecessor and H. erectus remains and apply ever improving techniques of genetic retrieval. Yet there is a chance that stretches of ancient DNA can be teased out of younger fossils.

Pushing back DNA sequencing: a Spanish cave bear

At the time, only 3 years ago, publication of the first full Neanderthal genome  seemed miraculous. Yet the apparent magic proved repeatable, including for an obscure but distinct group of extinct humans – the  Denisovans – known only from their DNA in a single pinkie bone. These advances astonished the world by showing that anatomically modern humans were capable of interbreeding with both groups; and did so that many people now living outside of Africa carry the genetic evidence. But the samples analysed for DNA were little more than 40 thousand years old. Older fossils of extinct animals have given up their genetic features, such as the wooly mammoth and a horse about 700 ka old, but only from samples frozen into permafrost at high northern latitudes.

The degradation of DNA over time seemed destined to limit palaeo-genetics, even when slowed down by natural freezing. The degradation breaks down any surviving genetic material into shorter and shorter fragments of the DNA molecule, ultimately to its atoms being recombined in new molecules of totally unrelated compounds through the chemical processes of fossilisation. Reassembling the fragments correctly becomes increasingly difficult the smaller they are. Few outside of a highly skilled specialists were optimistic of breaking the 100 ka barrier, even using frozen fossils. Unsurprisingly, having had such dramatic successes, the specialists continue to ride their luck and their ingenuity.

Excavations at the site of Gran Dolina, in Ata...
Excavations at Gran Dolina, in Atapuerca, Spain. (Photo credit: Wikipedia)

The cave complex of the Atapuerca Mountains  in northern Spain, whose sediments range in age from almost a million years ago to recent times, contain rich accumulations of human remains, including the pre-Neanderthal Homo heidelbergensis and H. antecessor dating back to more than 800 ka. If ever there was a magnet for archaeo-geneticists Atapuerca is definitely one. Moreover, physical anthropologists seem never to stop disputing their interpretations. Jesse Dabney of the now famous Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and co-workers from Britain, New Zealand, Spain and Australia are now beginning to report results. The first are from a cave bear (probably Ursos deningeri) known to be older than 300 ka (Dabney, J. and 10 others 2013. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments in one of its foreleg bones. Proceedings of the National Academy of Sciences, v. 110, doi/10.1073/pnas.1314445110). The bear’s mitochondrial DNA was pieced together from fragments as small as 50 base pairs, and shows its ancestry to bears (U. spelaeus) from the later Pleistocene that became extinct at about 28 ka.

reconstruction of a European cave bear (Ursus ...
Reconstruction of a European cave bear (Ursus spelaeus) (credit: Wikipedia)

It may be only a matter of time before human DNA emerges from the rich Atapuerca fossil hoard; indeed the authors strongly hint that they are working on that now.